Contacts of the strand formed by residues 241 - 245 (chain C) in PDB entry 5U03
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C VAL* 4.3 3.6 - - + -
216C CYS* 4.2 10.5 - - - -
222C LEU* 4.5 3.1 - - + -
227C LYS* 3.9 36.6 - - + +
230C ILE* 3.7 42.2 - - + -
231C SER 4.0 2.2 - - - +
236C VAL* 3.6 18.8 - - + -
237C GLU 2.9 17.8 + - - +
238C PRO* 2.9 23.7 - - + +
239C GLU 3.1 3.1 - - - +
240C GLN* 1.3 74.4 - - - +
242C ILE* 1.3 59.7 + - - +
243C CYS 3.7 1.7 + - - -
260C GLN* 4.5 4.7 - - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LEU* 3.7 35.7 - - + -
214C VAL 3.0 15.5 + - - +
215C VAL* 4.2 11.0 - - + -
216C CYS* 2.7 33.6 + - - +
239C GLU 3.7 13.0 - - - +
240C GLN 3.7 8.3 - - - +
241C VAL* 1.3 71.4 - - - +
243C CYS* 1.3 61.7 + - - +
244C VAL* 3.8 22.0 - - + -
257C LEU* 4.6 5.4 - - + -
260C GLN* 4.0 24.0 - - + +
262C VAL* 3.7 27.1 - - + -
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Residues in contact with CYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C CYS* 4.2 1.3 - - - -
218C CYS* 2.1 50.7 - - - -
221C PRO* 3.8 9.0 - - + -
222C LEU* 3.4 35.4 - - + +
227C LYS* 4.3 14.5 - - - +
241C VAL 3.7 4.4 + - - -
242C ILE* 1.3 73.0 - - - +
244C VAL* 1.3 59.4 + - - +
245C HIS* 3.8 7.6 + - - -
256C LEU* 3.7 16.3 - - - +
260C GLN* 4.1 15.4 + - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.3 19.1 - - + -
215C VAL* 3.6 26.5 - - + -
216C CYS 2.8 14.4 + - - +
217C ARG* 3.7 8.0 - - - -
218C CYS 3.0 19.0 + - - +
242C ILE* 3.8 16.8 - - + -
243C CYS* 1.3 74.1 - - - +
245C HIS* 1.3 67.1 + - - +
253C VAL* 4.5 10.3 - - + -
256C LEU* 3.8 22.2 - - + -
257C LEU* 4.5 5.4 - - + -
601C ATP 3.9 16.4 - - - +
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Residues in contact with HIS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C CYS* 3.4 9.9 - - - -
219C SER 3.3 12.5 + - - +
220C ASN 3.7 17.5 - - - +
221C PRO* 3.7 26.7 - - + +
243C CYS* 3.7 5.4 - - - -
244C VAL* 1.3 79.1 - - - +
246C ASP* 1.3 89.4 + - - +
247C VAL* 3.4 29.2 + - + +
252C ARG* 6.1 1.3 - - - -
256C LEU* 3.8 17.2 - - + +
259C GLU* 5.8 1.6 + - - -
601C ATP 3.8 6.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il